Variant Filters
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Filters by variant category.
Type |
Description |
---|---|
Small Variant |
SNVs, MNVs, insertions, deletions, and indels. |
Structural Variant |
Insertions, deletions,tandem duplications, and translocation breakends. |
Copy Number Variant |
Copy number variation, gain, or loss. |
Run of Homozygosity |
Regions of consecutive variant calls. |
Short Tandem Repeats |
Regions of repeating short DNA segments. |
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Type |
Description |
---|---|
SNV |
Single nucleotide variation. |
MNV |
Multiple nucleotide variation. |
Insertion |
Insertion of genomic sequence. |
Deletion |
Deletion of a genomic sequence. |
Indel |
Deletion and insertion of genomic sequence. |
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Type |
Description |
---|---|
Insertion |
Insertion of genomic sequence. |
Deletion |
Deletion of a genomic sequence. |
Tandem Duplication |
Duplication of genomic sequence in tandem. |
Translocation Breakend |
Structural variation that links breakpoints of two different points in the genome. |
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Type |
Description |
---|---|
Copy Number Variation |
The copy number is increased or decreased relative to the reference sequence. |
Copy Number Loss |
The copy number is less than the reference sequence. |
Copy Number Gain |
The copy number is greater than the reference sequence. |
Copy Number Neutral |
The copy number is the same as the reference sequence. |
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Filters data by the specified consequence.
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Filters data by the presence and location of start and stop alterations.
Consequence |
Description |
---|---|
Start Loss |
The loss of a start codon in the coding sequence. |
Stop Gained |
The gain of a stop codon in the coding sequence. |
Stop Loss |
The loss of a stop codon in the coding sequence. |
Incomplete Terminal Codon |
A change to at least one base of the final codon of an incomplete annotated transcript. |
Feature Elongation |
The variant causes the extension of a genomic feature. |
Feature Truncation |
The variant causes the reduction of a genomic feature. |
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Filters data by the affected splice site.
Type |
Description |
---|---|
Splice Acceptor Variant |
The variant affects the canonical splice acceptor site (last two bases of the 3ʹ end of the intron). |
Splice Donor Variant |
The variant affects the canonical splice donor site (first two bases of the 5ʹ end of the intron). |
Splice Region Variant |
An indel or substitution in a noncoding splice region of the gene. |
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Type |
Description |
---|---|
Frameshift Variant |
An insertion or deletion in which the number of base pairs is not divisible by 3, causing a frame disruption. |
Inframe Deletion |
A deletion that does not disrupt the reading frame. |
Inframe Insertion |
An insertion that does not disrupt the reading frame. |
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Type |
Description |
---|---|
Missense Variant |
A single base pair substitution that results in the translation of a different amino acid at that position. |
Protein Altering Variant |
The variant has a protein-altering coding consequence. |
Coding Sequence Variant |
The variant changes the coding sequence. |
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Filters data by the variant relationship to a gene.
Type |
Description |
---|---|
Intergenic Variant |
The variant position is not covered by any gene transcript. |
Upstream Gene Variant |
The variant position is within 5 kb upstream of the defined transcript start coordinate. |
Downstream Gene Variant |
The variant position is within 5 kb downstream of the defined transcript end coordinate. |
Intron Variant |
The variant occurs within an intron. |
3-prime UTR Variant |
The variant is in the 3ʹ untranslated region of a gene. |
5-prime UTR Variant |
The variant is in the 5ʹ untranslated region of a gene. |
Noncoding Transcript Exon Variant |
The variant changes the noncoding exon sequence in a noncoding transcript. |
Noncoding Transcript Variant |
The variant occurs in a noncoding RNA gene. |
Synonymous Variant |
The variant does not affect the primary amino acid sequence of the translated protein. |
Start Retained Variant |
At least one base in the start codon is changed, but the start codon remains. |
Stop Retained Variant |
At least one base in the terminator codon is changed, but the terminator remains. |
Mature MiRNA Variant |
The variant occurs within a mature miRNA sequence. |
NMD Transcript Variant |
The variant is in a transcript and is the target of nonsense‑mediated decay (NMD). |
Regulatory Region Ablation |
A deletion of a region that contains a regulatory region. |
Regulatory Region Amplification |
An amplification of a region that contains a regulatory region. |
Regulatory Region Variation |
The variant occurs in a regulatory region. |
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Filters data by the transcript consequence.
Consequence |
Description |
---|---|
Transcript Variant |
The variant changes the structure of the transcript. |
Transcript Ablation |
A deletion of a region that contains a transcript feature. |
Transcript Amplification |
An amplification of a region that contains a transcript. |
Transcript Truncation |
A truncation of a region that contains a transcript. |
Feature Elongation |
The variant causes the extension of a genomic feature. |
Feature Truncation |
The variant causes the reduction of a genomic feature. |
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Filters data by the gene fusion consequence.
Consequence |
Description |
---|---|
Unidirectional Gene Fusion |
A fusion of two genes on the same strand. |
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Filters data by the transcript consequence.
Consequence |
Description |
---|---|
Transcript Variant |
The variant changes the structure of the transcript. |
Transcript Ablation |
A deletion of a region that contains a transcript feature. |
Transcript Amplification |
An amplification of a region that contains a transcript. |
Transcript Truncation |
A truncation of a region that contains a transcript. |
Feature Elongation |
The variant causes the extension of a genomic feature. |
Feature Truncation |
The variant causes the reduction of a genomic feature. |
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Filters data by the copy number consequence.
Type |
Description |
---|---|
Copy Number Increase |
The copy number is increased relative to the reference sequence. |
Copy Number Decrease |
The copy number is decreased relative to the reference sequence. |
Copy Number Change |
The copy number is increased or decreased. |
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Filters data by short tandem repeat consequences: expansion, contraction, and change.
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Filters data by splice mutation probability, as predicted by deep learning engines.
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Filters by specified chromosomes. If no chromosome is selected, the chromosome filter is not applied.
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Filters by gnomAD constraint metrics.
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Filters by labels provided in a custom annotation file.
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Filters by specified genes and genes related to specified phenotypes. Gene names are case-sensitive.
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Filters by the status of the SMN and STR calls for each subject.
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Filters by specified regions. The input format is chr#:start-end, with multiple regions separated by spaces or new lines.
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Filters by the ClinGen haploinsufficiency evidence classification.
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Excludes small variants in low complexity regions (LCRs).
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Filters data by the positive difference in Variant Read Frequency between proband and mother. Mitochondrial variants are typically maternally inherited, though the variant read frequency can differ between parent and proband. An increase in variant read frequency for a pathogenic mitochondrial variant might result in mitochondrial disorder.
The input value range is 0–1, with precision to 0.0001.
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Filters data by the mode of inheritance. For information about inheritance criteria, see Mode of Inheritance Logic .
Selecting an inheritance option enables one or more subfilters to select from.
Mode of Inheritance |
Description |
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---|---|---|---|---|---|---|---|
De Novo (DN) |
The variant is not present in the parents. |
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Dominant (DOM) |
At least one parent is affected and the variant is present in all affected subjects. |
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Present in Proband (PR) |
The variant is present in the proband subject. |
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Recessive (RSG or RCH) |
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Filter |
Description |
---|---|
Assume Complete Penetrance |
Excludes variants that are homozygous or hemizygous in unaffected individuals. This option is used to find variants for which complete penetrance is expected. |
Exclude Ambiguous |
Excludes RCH variants that have ambiguous inheritance, if de novo variants are absent or have been filtered out. |
Exclude Low Confidence |
Excludes de novo variants that are classified as low confidence. |
Exclude Observed Homozygotes |
Excludes variants observed in a homozygous state within the pedigree. |
In Affected |
Excludes variants that are not present in all affected individuals. |
Not in Unaffected |
Excludes variants that are present in unaffected individuals. |
Same Genotype in Affected |
Returns variants that are homozygous, hemizygous, or hemizygous diploid loss in all affected individuals. |
Shared Variant in Affected |
Returns RSG variants that are present in all affected individuals or RCH variants where at least one variant from a given variant set for a transcript is present in all affected individuals. |
Strict |
Returns only recessive variants that are inherited from both parents. |
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Filters data by presence in the OMIM gene database.
Item |
Description |
---|---|
Present in OMIM |
An OMIM entry exists for the gene. |
Has associated OMIM phenotypes (including ?) |
A provisional relationship exists between the phenotype and a matching gene at the transcript level. |
Has associated OMIM phenotypes (excluding ?) |
A relationship exists between the phenotype and a matching gene at the transcript level. |
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Filters data by the pathogenic evidence from ClinVar or your knowledge base.
NOTE
Inclusion and exclusion filters capture all variants that have associations for the selected pathogenicity, regardless of any other pathogenicities associated with the variant. For example, a filter that excludes benign pathogenicities also excludes any variants that have both benign and pathogenic associations.
Item |
Description |
---|---|
P (Pathogenic) |
Segregates with disease in multiple unrelated cases with control data. The variant is in a highly conserved region. Functional studies or other evidence indicate a deleterious effect on gene expression. |
LP (Likely Pathogenic) |
Reported in some case studies with or without control data. The variant is in a highly conserved region. Functional studies or other evidence highly suggest a deleterious effect on gene expression. |
VUS (Variant of Unknown Significance) |
Nothing about this variant has been reported, or reported information is incomplete or contradictory. |
LB (Likely Benign) |
Functionally normal. Reported in a few cases with little or no control data. The variant might be nonconserved and predicted to be tolerated. Based on disease prevalence and penetrance information, the variant frequency is higher than expected in the general population. |
B (Benign) |
Functionally normal. Reported at high frequency in control data and does not segregate with disease. The variant might be nonconserved and predicted to be tolerated. |
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Filters selected ClinVar pathogenicities by review status.
# of Stars |
Description |
---|---|
1 |
Single submitter or multiple submitters with conflicting evidence. |
2 |
Multiple submitters, no conflicting evidence. |
3 |
Reviewed by expert panel. |
4 |
Practice guideline. |
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Filters data based on the allele frequency in population studies. Large variants (eg, CNVs and SVs) are filtered based on aggregate frequency. The aggregate frequency is calculated as the sum of all allele frequencies for annotations where the number of alleles is at least 300 and the reciprocal overlap is above the threshold set in the test definition.
The available population databases vary depending on the selected variant type. For detailed information about the population frequencies, see Population Data.
• | To set a variant filter for frequency values, enter a value from 0–1 in the field. Frequency values support precision to 0.00001. |
• | To filter by the average frequency across all options in a database, enter a value in the All Populations field. |
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Filters data by whether variants pass filter.
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Filters data by read metrics.
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Filters data by variant length. Supports decimal values for sizes < 1 Mbp, with precision to 0.001.
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Filters by the ClinGen triplosensitivity classification.
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Zygosity |
Description |
---|---|
Homozygous |
Variants that are present on both alleles. |
Heterozygous |
Variants that are present on one of two alleles. |
Hemizygous |
Variants that are present on one allele for non-diploid regions. |
Hemizygous Diploid Loss |
Variants that are present on one allele, where the other allele is deleted due to a copy number variation. |